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- PDB-5c8o: Crystal structure of MoCVNH3 variant (Mo0v) -

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Basic information

Entry
Database: PDB / ID: 5c8o
TitleCrystal structure of MoCVNH3 variant (Mo0v)
ComponentsMoCVNH3 variant
KeywordsSUGAR BINDING PROTEIN / lectin / N-acetylglucosamine / CVNH
Function / homology
Function and homology information


Glycine zipper 2TM domain / Glycine zipper 2TM domain / Membrane-bound Lytic Murein Transglycosylase D; Chain A / LysM domain / HIV-inactivating Protein, Cyanovirin-n / Cyanovirin-N / Cyanovirin-N / Cyanovirin-N superfamily / CVNH domain / CVNH ...Glycine zipper 2TM domain / Glycine zipper 2TM domain / Membrane-bound Lytic Murein Transglycosylase D; Chain A / LysM domain / HIV-inactivating Protein, Cyanovirin-n / Cyanovirin-N / Cyanovirin-N / Cyanovirin-N superfamily / CVNH domain / CVNH / Lysin motif / LysM domain superfamily / LysM domain profile. / LysM domain / LysM domain / Roll / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
LysM domain-containing protein / LysM domain-containing protein
Similarity search - Component
Biological speciesMagnaporthe oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsKoharudin, L.M.I. / Gronenborn, A.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM080642 United States
CitationJournal: Structure / Year: 2015
Title: Structural Insight into Fungal Cell Wall Recognition by a CVNH Protein with a Single LysM Domain.
Authors: Koharudin, L.M. / Debiec, K.T. / Gronenborn, A.M.
History
DepositionJun 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Nov 11, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MoCVNH3 variant


Theoretical massNumber of molelcules
Total (without water)17,3461
Polymers17,3461
Non-polymers00
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.411, 51.075, 43.243
Angle α, β, γ (deg.)90.00, 110.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MoCVNH3 variant


Mass: 17345.996 Da / Num. of mol.: 1 / Mutation: UNP residues 175-341
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnaporthe oryzae (rice blast fungus) / Plasmid: pET15B / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: L7JBY8, UniProt: G4N991*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: ~8-10 % (w/v) PEG 3350, 0.1 M sodium phosphate-citrate buffer, pH 4.2, 0.2 M NaCl
PH range: 4.2-5.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 1, 2011
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.09→37.41 Å / Num. obs: 9051 / % possible obs: 99.2 % / Redundancy: 2.66 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 10.5
Reflection shellResolution: 2.09→2.16 Å / Redundancy: 1.68 % / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 2.1 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0044refinement
d*TREKdata reduction
Cootmodel building
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L5B,1Y7M

1l5b

1y7m


Resolution: 2.09→37.41 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.912 / SU B: 5.413 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28115 906 10 %RANDOM
Rwork0.22041 ---
obs0.22622 8145 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.661 Å2
Baniso -1Baniso -2Baniso -3
1--11.44 Å20 Å2-10.15 Å2
2---12.68 Å2-0 Å2
3---24.12 Å2
Refinement stepCycle: 1 / Resolution: 2.09→37.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1201 0 0 102 1303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0211253
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0341.9211696
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.425158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.13322.59777
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8815203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4351519
X-RAY DIFFRACTIONr_chiral_restr0.070.2171
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021020
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2841.5749
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.53921193
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.8853504
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.4564.5499
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.09→2.144 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 76 -
Rwork0.267 562 -
obs--96.23 %

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